How do I set up a complicated rig correctly for linking? (Advanced)
Take a look at this:

Rigging question about Spline IK and having all controls on one armature

It's an example of rig structure with multiple armatures inside parented, to avoid dependency issues.

The trick is to have all the controls the animator will interact with inside one master armature, and to copy these bones with constraints to the other armatures where they do things. This way, you only need to make a proxy of this master armature when the rig is linked and everything else becomes inner workings of the rig.

This should remedy any parent breaking problems when creating proxy rigs.